South Sudan town back under govt control

South Sudan's army has reclaimed control of a town destroyed in a bloody cattle vendetta that sent thousands fleeing into the bush and threatened the stability of the world's newest state.

A column of some 6000 armed youths from the Lou Nuer tribe marched on the remote town of Pibor in troubled Jonglei state, home to the rival Murle people, who they blame for cattle raiding and have vowed to exterminate.

"Pibor is under the full control of the government, and the Lou Nuer have been ordered to return to their homes, and they are starting to do so," Information Minister Barnaba Marial Benjamin said on Tuesday.

Gunmen burned thatched huts and looted a hospital run by Doctors Without Borders in the worst flare-up in a dispute that has left more than 1000 dead in recent months and threatened to destabilise the fledgling nation.

John Boloch Kumen, from the government-appointed Peace and Reconciliation Commission, has visited the village of Lekongele, some 30 kilometres north of Pibor as part of an assessment team.

"No single house was left, the whole town was devastated ... seven people were burned in their tukuls (thatch huts), all of them women," Kumen said, adding that two churches, a school and a health centre were razed to the ground.

"What was left was only the vultures and the trees," he added.

The government and the United Nations - which has warned the ethnic violence could lead to a "major tragedy" - were beefing up their forces in the area.

Lise Grande, the UN humanitarian co-ordinator for South Sudan, said "probably well over 20,000" people had fled into the bush "running for their lives and looking for safety".

Officials fear the fighting has left scores of people dead, while the UN has flown the wounded to the capital Juba.

Unconfirmed reports based on survivor accounts suggested up to 150 people, largely women and children, were hunted down and killed after fleeing Pibor.

"There are many casualties, people that have been killed," said Pibor Commissioner Joshua Konyi. "We are still waiting for the reports to confirm."

Just one health clinic remains to provide healthcare for some 160,000 people in Pibor county, after Pibor hospital and a clinic at Lekongole run by Doctors Without Borders were looted.

Parthesarathy Rajendran, MSF head of mission in South Sudan, warned that the longer people stay in the bush the "more serious it will become for people who are injured or sick".

"They fled in haste and have no food or water, some of them doubtless carrying wounds or injuries, and now they are on their own, hiding, beyond the reach of humanitarian assistance," Rajendran said in a statement.

Ethnic violence, cattle raids and reprisal attacks in the vast eastern state left more than 1100 people dead and forced some 63,000 from their homes last year, according to UN reports based on local authorities and assessment teams.

Tit-for-tat cattle raiding is common in a grossly underdeveloped region awash with guns and left in ruins by decades of war with northern Sudanese forces, who fuelled conflict by backing proxy militia forces across the south.